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docs: Add info about the sample column concatinating groups #144

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docs: Add info about the sample column concatinating groups #144

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6 changes: 6 additions & 0 deletions docs/usage.md
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Expand Up @@ -50,6 +50,12 @@ TREATMENT_REP3,AEG588A6_S6_L004_R1_001.fastq.gz,

An [example samplesheet](../assets/samplesheet.csv) has been provided with the pipeline.

:::info
The sample column is essentially a concatenation of the group and replicate columns. If all values of sample have the same number of underscores, fields defined by these underscore-separated names may be used in the transcript identification produced by the pipeline, to regain the ability to represent different groupings.

`GM_0h` and `GM_1h` would be grouped for example but `GM0h` and `GM1h` would go through individual transcript identification
:::

## Alignment Options

By default, the pipeline uses [BWA](https://bio-bwa.sourceforge.net/) (i.e. `--aligner bwa`) to map the raw FastQ reads to the reference genome. Research as to which aligner works best with Nascent Transcript and Transcription Start Site assays is pending.
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